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    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

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    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

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    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

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    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

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    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

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    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

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    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

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    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

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Data & Tools
Home › Data & Tools › Data Management Practices and Resources

Data Management Practices and Resources

Read JGI’s Data Policy

Read the DOE Office of Science Statement on Digital Data Management

Current Data Management Practices

Raw sequence data—Raw data produced by the DOE JGI’s sequencing platforms are base-called in real time and primary (image) data are discarded shortly after base-calling is complete.  Sequence data are stored as FASTQ files containing the linear sequence and associated quality scores.   All primary sequence data receive automated quality control screening to assess sequence quality and quantity, identify major contamination, and confirm that the data generated correspond to the expected organism/environment being sequenced.  For most sequencing projects, raw sequence data is made available to registered users through the genome-specific portal web page and are submitted to NCBI’s Sequence Read Archive (SRA) as soon as the embargo defined by the JGI Data Policy has ended.

Processed sequence data—For most user projects, the DOE JGI conducts standard post-sequencing analyses that vary by project type (see Product Offerings).  These analyses and associated metadata are available for download from project-specific data portals to the DOE JGI data users after the embargo has ended. User-selected subsets of public data can also be downloaded from the DOE JGI’s comparative analysis platforms as described in Data Resources below.  Beginning in fall 2013 users wishing to download data from the DOE JGI portals will be required to register with the DOE JGI.

Project metadata—Every user project has associated metadata that are important for interpretation of the data produced.  These include, for example, authors of the data, PI contact information, detailed sample information and details of analyses performed.  These data will be served with processed data from the DOE JGI’s data portals whenever possible, however metadata for older legacy projects may be limited.

Data archive and back-up—All data available for download by users is automatically archived onto a high-speed tape system located at the National Energy Research Scientific Computing facility (NERSC).  A second redundant copy of these data is also stored on high-speed tape (but not on the same cassette!).  Typical retrieval times range from minutes to hours depending primarily on file size.

Data Management Resources

The DOE JGI provides some resources to users to facilitate analysis of genomic data produced outside of the DOE JGI or to allow post-hoc analysis of DOE JGI data.  Because these resources are supported through public funds it is expected that such analyses and externally created data managed with these resources will be made public at the time of publication.  The user bears sole responsibility for providing and maintaining public access to these data and analyses.

Phytozome —The DOE JGI’s comparative genomics platform for plants allows user-driven filtering of plant genome data by characteristics of interest that are then downloadable by individual users.  Phytozome does not currently keep these analyses nor support their display for other users.  Phytozome supports the display of user-provided genome tracks that are compatible with GBrowse, but does not generally display these tracks for other users.  By mutual agreement between JGI and the data providers, Phytozome may display non-DOE JGI genomes for comparative purposes or additional genome-anchored data for DOE JGI genomes. The DOE JGI will make these data public and downloadable following the embargo, but responsibility for depositing these data in public repositories resides with the data provider.

MycoCosm and PhycoCosm —The DOE JGI’s comparative genomics platforms for fungi and algae support user-driven filtering of comparative genomics data by characteristics of interest that are downloadable by individual users.  These platforms support manual curation of genome annotations by registered users who have received specific training.  These annotations are in turn served to the user community.  MycoCosm and PhycoCosm may display genomes and annotations created elsewhere by mutual agreement between JGI and the owners of the external genome data. JGI will make these data public and downloadable following the embargo, but responsibility for depositing these data in public repositories resides with the data provider.

Integrated Microbial Genomes platform (IMG)—IMG supports user-driven filtering of comparative genomics data by characteristics of interest and maintains results for users. Results of comparative analyses are downloadable and may be shared with other users within the IMG system.  Responsibility for providing public access to these data at the time of publication is the sole responsibility of the user.  Isolate genomes, single cell genomes and metagenome datasets produced elsewhere may be uploaded for annotation and analysis within IMG. Data must be made public at the time of publication and this responsibility lies with the user.

Genomes OnLine Database (GOLD)—GOLD is an online database of worldwide genome projects and associated metadata that is maintained for the public by the DOE JGI. The data are filterable and downloadable.  Users may register their genome projects in GOLD, but must agree to make the registration and associated metadata publicly available at the time of publication.  Registration of non-DOE JGI genome projects with NCBI or other public registries is the sole responsibility of the user.

DOE JGI’s Policy on Microbial Genbank Submissions

Microbial genome sequencing projects become eligible for preparation for submission to Genbank when they become public in the Integrated Microbial Genomes system following the embargo. This includes sequences from both cultured organisms and single cells sequenced at DOE JGI only*.

All eligible projects are prepared as WGS submissions. Although JGI has been submitting annotated genomes to Genbank in the past, moving forward we will only support WGS submissions and will serve annotations through IMG.

For questions, please contact Galina Ovchinnikova.

* Please note that genomes submitted by external users for annotation and comparative analysis in IMG are not automatically submitted to Genbank.

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